rs140462332
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_001843.4(CNTN1):c.2598C>G(p.Ala866Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000214 in 1,613,946 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 1 hom. )
Consequence
CNTN1
NM_001843.4 synonymous
NM_001843.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.303
Publications
0 publications found
Genes affected
CNTN1 (HGNC:2171): (contactin 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
CNTN1 Gene-Disease associations (from GenCC):
- Compton-North congenital myopathyInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
- schizophreniaInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 12-41025224-C-G is Benign according to our data. Variant chr12-41025224-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 258195.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.303 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00112 (171/152242) while in subpopulation AFR AF = 0.00366 (152/41540). AF 95% confidence interval is 0.00318. There are 0 homozygotes in GnomAd4. There are 76 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.2598C>G | p.Ala866Ala | synonymous_variant | Exon 21 of 24 | ENST00000551295.7 | NP_001834.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.2598C>G | p.Ala866Ala | synonymous_variant | Exon 21 of 24 | 1 | NM_001843.4 | ENSP00000447006.1 | ||
CNTN1 | ENST00000347616.5 | c.2598C>G | p.Ala866Ala | synonymous_variant | Exon 20 of 23 | 1 | ENSP00000325660.3 | |||
CNTN1 | ENST00000348761.2 | c.2565C>G | p.Ala855Ala | synonymous_variant | Exon 19 of 22 | 1 | ENSP00000261160.3 | |||
CNTN1 | ENST00000550305.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00112 AC: 171AN: 152124Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
171
AN:
152124
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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GnomAD2 exomes AF: 0.000366 AC: 92AN: 251082 AF XY: 0.000280 show subpopulations
GnomAD2 exomes
AF:
AC:
92
AN:
251082
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.000120 AC: 175AN: 1461704Hom.: 1 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 727156 show subpopulations
GnomAD4 exome
AF:
AC:
175
AN:
1461704
Hom.:
Cov.:
31
AF XY:
AC XY:
76
AN XY:
727156
show subpopulations
African (AFR)
AF:
AC:
100
AN:
33456
American (AMR)
AF:
AC:
20
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39692
South Asian (SAS)
AF:
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
AC:
1
AN:
5764
European-Non Finnish (NFE)
AF:
AC:
37
AN:
1111882
Other (OTH)
AF:
AC:
17
AN:
60386
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
12
25
37
50
62
0.00
0.20
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0.95
Allele balance
Age Distribution
Exome Het
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Age
GnomAD4 genome AF: 0.00112 AC: 171AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74436 show subpopulations
GnomAD4 genome
AF:
AC:
171
AN:
152242
Hom.:
Cov.:
32
AF XY:
AC XY:
76
AN XY:
74436
show subpopulations
African (AFR)
AF:
AC:
152
AN:
41540
American (AMR)
AF:
AC:
11
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5180
South Asian (SAS)
AF:
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
AC:
0
AN:
10612
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6
AN:
68022
Other (OTH)
AF:
AC:
2
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
9
19
28
38
47
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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Age
Alfa
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EpiCase
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Mar 10, 2020
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Jun 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
CNTN1: BP4, BP7 -
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Compton-North congenital myopathy Benign:1
Nov 18, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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